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Merge pull request #1440 from ellio167/kim-simulator-models

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Develop native support for KIM simulator models
This commit is contained in:
Axel Kohlmeyer
2019-07-30 10:53:58 -04:00
committed by GitHub
parent 3eadfa15ef c9f3f99ee8
commit 8fa4efa08e
53 changed files with 4536 additions and 1611 deletions
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examples/kim/.gitignore vendored Normal file
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/kim.log

10
examples/kim/in.kim.lj.newton-on → examples/kim/in.kim-ex.melt
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@ -14,20 +14,14 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton on
kim_init LennardJones_Ar real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
pair_style kim LennardJones_Ar
pair_coeff * * Ar
kim_interactions Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom

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examples/kim/in.kim-pm-query.melt Normal file
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# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

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examples/kim/in.kim-pm.melt Normal file
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# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

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examples/kim/in.kim-sm.melt Normal file
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# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions O
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

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examples/kim/in.kim.lj.lmp.newton-off
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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton off
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

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examples/kim/in.kim.lj.newton-off
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# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton off
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
pair_style kim LennardJones_Ar
pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

4
examples/kim/in.kim.lj.lmp.newton-on → examples/kim/in.lammps.melt
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@ -8,9 +8,7 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton on
units real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}

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examples/kim/in.query
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# example for performing a query to the OpenKIM test database to retrieve
# a parameter to be used in the input. here it requests the aluminium
# lattice constant for a specific test used for a specific model and then
# assigns it to the variable 'latconst'
units metal
info variables out log
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
info variables out log
lattice fcc ${latconst}

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examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1
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LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.004499 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54
Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90
Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23
Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00
Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95
Other | | 0.01091 | | | 0.37
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2370499
Ave neighs/atom = 74.0781
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4
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@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.001039 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63
Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22
Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89
Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01
Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89
Other | | 0.02618 | | | 3.36
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 630904 ave 632094 max 628209 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 2523614
Ave neighs/atom = 78.8629
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1
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@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003479 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26
Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65
Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08
Other | | 0.01094 | | | 0.50
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2126875
Ave neighs/atom = 66.4648
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4
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@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000919 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63
Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58
Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32
Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01
Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47
Other | | 0.006263 | | | 0.99
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 531719 ave 533273 max 529395 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2126875
Ave neighs/atom = 66.4648
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

59
examples/kim/log.06Feb2019.in.kim.lj.newton-off.1
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@ -1,59 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003446 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05
Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58
Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82
Other | | 0.01032 | | | 0.34
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.06Feb2019.in.kim.lj.newton-off.4
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@ -1,65 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000921 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52
Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91
Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74
Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01
Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17
Other | | 0.005874 | | | 0.66
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

59
examples/kim/log.06Feb2019.in.kim.lj.newton-on.1
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LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003089 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58
Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82
Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41
Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00
Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81
Other | | 0.01132 | | | 0.37
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.06Feb2019.in.kim.lj.newton-on.4
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LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000893 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53
Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85
Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82
Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00
Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04
Other | | 0.006797 | | | 0.75
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

34
examples/kim/log.22Mar2019.query.g++.1
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LAMMPS (28 Feb 2019)
# example for performing a query to the OpenKIM test database to retrieve
# a parameter to be used in the input. here it requests the aluminium
# lattice constant for a specific test used for a specific model and then
# assigns it to the variable 'latconst'
units metal
info variables out log
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:56 2019
Variable information:
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
info variables out log
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:57 2019
Variable information:
Variable[ 0]: latconst , style = string , def = 4.03208274841
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
lattice fcc ${latconst}
lattice fcc 4.03208274841
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
Total wall time: 0:00:00